design and order fluorescent primers for debugging construction plasmid PCR, cutting and ligation. Pacific blue and Alexa Fluor 488 appear to work well with UV excitation. Prefix-R and Suffix-F ordered.

Miniprep of pRML1, pRML2, pYAC4. Design and order sequencing primers and half of the needed construction primers for YAC left and right arms. Remainder awaiting sequencing results.

29 August 2006

Order medium components (Spencer 93)

Sequencing primers for pRML1, pRML2

pBluescript II SK+

pCGS966

URA3

TRP

ARS1

ARSH4

CEN4

Construct parts from Left, Right telomere, Left, Right chromosome ends

Rocha paper on survey of recombination systems in sequenced bacteria. Florum has RecO, RecR, but not RecF in the RecFOR system. RecA present. RecD present. RuvAB present, ruvC not, but replaced with RecU. yqgF gene part of the recomination system. PriA missing. RecBC missing, RecD form is different from the form found in organisms with RecBC also.

Received yeast strains and plasmids from Weiss lab. Confirmed that they cannot PCR through the centromere CDS II region.

Codon usage of the P1014 cassette. CTC codon (Lys) is rare and used 4+ times. CGG is not present in the CDS. Three GATC sequences.

Compromise codon usage: multiply codon probabilities for corresponding codons from each organism, then take the square root (geometric mean). Renormalize within each amino acid to establish new relative probabilities.